Is there a tool to pertub a secondary structure of a RNA by permutating its nucleotide sequence. In my case, I've a sequence encoding mutliple miRNAs (each pre-miR has a hairpin structure). I want to delete each of the hairpin structures by changing as little as possible the sequence.
The goal is to take this sequence encoding multiple miRNAs, to modify it to perturb the structure to delete the hairpins and to put it in a lentiviral vector and to see if it is processed
I posted a more biological question for the same topic on biology.stackexchange : http://biology.stackexchange.com/questions/680/rna-sequence-modification-which-newly-pattern-ive-to-avoid
Thanks a lot,